Let's say you've got one ChildSt inheriting from BaseSt1 and BaseSt2. Your XML file will then contain
<Stereotype name="ChildSt" ...
generalizes="BaseSt1" baseStereotypes="BaseSt1 BaseSt2"/>
In order for generalization between stereotypes in different profiles to work, you need to qualify the baseStereotypes reference. EA (10.0.1009) does not do this for you, so what you end up with is still a maintenance nightmare, albeit one with a slightly different monster (post-generation manual XML file editing).
You should also note that only one base stereotype is listed as generalizes. Exactly what effect that has I'm not sure. Possibly it controls which RefGUID tags the child may be used in (in this case, it could then be used in tags specifying BaseSt1 but not in tags specifying BaseSt2), but that's conjecture.
Ways around: I don't know of one, I'm afraid. Unless you can separate your stereotypes into completely separate inheritance hierarchies, I think you might be stuck. So it may be necessary to decide which evil is lesser: a single large profile, or duplication of tags in separate profiles. (Of course, within each profile you can set up the corresponding inheritance hierarchy to minimize the effect.)
As to that, and this is more in response to ZuluTen, having several different profiles in the same MDG Technology is not just possible, but usually a good idea (unless you run into an issue like above).
I have not had any good experiences placing packages inside a profile, but the other way around works just fine. So you wouldn't nest profiles inside each other, but place the different profiles in a single containing package. That package is only there for convenience in your MDG Technology project (you are developing your MDG Technology in a completely separate project, aren't you?), you never generate anything from it.
My MDG Technology projects typically contain a structure like this:
"MDG Technology name" (root node)
|- Profiles
| |- «profile» UML Profile 1
| |- «profile» UML Profile 2
|- Toolboxes
| |- «profile» Toolbox 1
| |- «profile» Toolbox 2
|- Diagrams
| |- «profile» "MDG Technology name" (if there are only a small number of diagrams)
|- Learning Center
| |- «profile» Learning Center Pane 1
... with additional levels as required; typically there may be some subdivision of toolboxes if there are a large number of diagrams. Only the «profile» packages are ever saved as profiles, the others are just structural sugar.
The model structure is mirrored in the directory structure on the disk, of course, which makes the MDG Technology creation process more convenient.
A word of warning: while moving stereotypes into separate profiles can usually be done in a production environment with little risk, shuffling diagram types between profiles cannot. This is because the stereotypes are only stored with their simple names, but the custom diagram type is stored as a qualified name inside each diagram's StyleEx column.
HTH,
/Uffe